Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure
Open accessAbstract
BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.
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The main selective effects on codon context are found in the nucleotides following the codon in the 3' direction.
“The main selective effects on codon context are found in the nucleotides following the codon in the 3' direction [16,18,19,22].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [22]
The Introduction (page unavailable) says the strongest neighboring-nucleotide influence arises from the interplay between a codon’s last nucleotide and the next codon’s first nucleotide. The Results section on genome and translation biases likewise finds that this pair discriminates codon-pair preferences. These passages support an important role for a nucleotide in the 3′ direction, but not the claim that the main effects reside in the following nucleotides alone. (LLM, conf=0.82)
Experimental — accuracy not yet measuredClosely related species have similar codon pair bias.
“A comparison of CPSs derived from different organisms (Figure 1; Figure S1) confirmed that closely related species have a similar codon pair bias (CPB) (Moura et al., 2007;Shen et al., 2015).”
From Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias (2016) · cites this paper as Moura et al., 2007
Dinucleotide bias appears to be linked with codon pair bias.
“Dinucleotide bias also appears to be linked with codon pair bias (Moura et al., 2007;Shen et al., 2015), but this relationship has not been thoroughly explored.”
From Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias (2016) · cites this paper as Moura et al., 2007
Specific preferred or avoided nucleotide patterns differ among species.
“It has been found that the specific preferred or avoided nucleotide patterns differ among species [16,22].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [22]
The only universal context selection rule found to cover all three domains of life was the avoidance of most codon pairs of the nnUAnn type, which was suggested to result from rejection of TA dinucleotides in DNA sequences.
“Previously, the only universal context selection rule found to cover all three domains of life was the avoidance of most codon pairs of the nnUAnn type, which was suggested to result from rejection of TA dinucleotides in DNA sequences [22].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [22]
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Nucleotide sequence conservation in paramyxoviruses; the concept of codon constellation
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Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy
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Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts
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A New Study on Biclustering Tools, Biclusters Validation and Evaluation Functions
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FOXC2 and FLT4 Gene Variants in Lymphatic Filariasis
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A Comparative Study of Clustering and Biclustering of Microarray Data[
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A Codon-Pair Bias Associated With Network Interactions in Influenza A, B, and C Genomes
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Self-citationCodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences
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Tailoring the Immune Response via Customization of Pathogen Gene Expression
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Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration
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Visualizing Codon Usage Within and Across Genomes: Concepts and Tools
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Mixture models of geometric distributions in genomic analysis of inter-nucleotide distances
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Self-citationComparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias
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Codon usage bias analysis for the coding sequences of Camellia sinensis and Brassica campestris
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Codon usage bias analysis of genes linked with esophagus cancer
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Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson’s Disease
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Sequences Promoting Recoding Are Singular Genomic Elements
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Self-citationA New Survey on Biclustering of MicroArray Data
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PECULIARITIES OF codon CONTEXT AND SUBSTITUTION WITHIN STREPTOMYCETE GENOMES
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Cramér Coefficient in Genome Evolution
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- Authors
- Moura, G., Pinheiro, M., Arrais, J., Gomes, A. C., Carreto, L., Freitas, A., Oliveira, J. L., & Santos, M. A. S.
- Affiliations
- Centro de Estudos do Ambiente e do Mar (PT)
- University of Aveiro (PT)
- Corresponding author
- Santos, Manuel A. S.
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-09-05
- Volume
- 2
- Issue
- 9
- Pages
- e847
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC1952141
- OpenAlex
- W2058323291
- Cited by
- 107
- References
- 55
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 5 · 2023: 5 · 2022: 5 · 2021: 9 · 2020: 5 · 2019: 2 · 2018: 2 · 2017: 4 · 2016: 9 · 2015: 12 · 2014: 13 · 2013: 6 · 2012: 6
- FWCI
- 1.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, cc-by)
- Funders
- Fundação para a Ciência e a Tecnologia
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- codon usage, translation machinery, DNA methylation, trinucleotide repeats, comparative genomics, three domains of life
- MeSH terms
- Codon, RNA, Bacterial, RNA, Messenger, Open Reading Frames, Evolution, Molecular, RNA, Archaeal
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